rs888663

Positions:

• chr19-18374112-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.836 in 152,078 control chromosomes in the GnomAD database, including 53,320 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.84 (53320 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127014 AN: 151960 Hom.: 53272 Cov.: 31

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.814

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.836 AC: 127118 AN: 152078 Hom.: 53320 Cov.: 31 AF XY: 0.837 AC XY: 62160 AN XY: 74306

Gnomad4 AFR AF: 0.892

Gnomad4 AMR AF: 0.834

Gnomad4 ASJ AF: 0.849

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.881

Gnomad4 NFE AF: 0.804

Gnomad4 OTH AF: 0.808

Alfa AF: 0.808 Hom.: 100207

Bravo AF: 0.837

Asia WGS AF: 0.760 AC: 2644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.079
DANN	Benign	0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs888663; hg19: chr19-18484922;